We calculated the prevalence of the metabolically healthy but obese (MHO) phenotype in (n = 9177) British men (age 48.9 ± 7.4 years) attending preventive health screening between 2000 and 2009. We examined differences in cardiorespiratory fitness (Fitness) and self-reported physical activity levels, according to whether the men were metabolically healthy (< 2 components of the metabolic syndrome), and by BMI category (normal-weight, overweight, obese). Fitness was estimated from treadmill exercise as VO2peak and classified as: Low, Moderate, or High using age-specific cut-offs. We identified 21.6% of our sample as obese, of whom 83.1% were metabolically healthy. Compared with the metabolic unhealthy obese (MUO; 3.7% of sample), MHO phenotypes were fitter (effect size d = 0.21) and were more physically active (d = 0.31). Logistic regression showed high fitness (OR = 2.40, 95% CI 1.38–4.19), and being physically active (OR = 1.71, 95% CI 1.14–2.56) to be independently associated with the MHO phenotype. Our findings agree with US data suggesting that higher cardiorespiratory fitness is a characteristic of the MHO phenotype. Our finding that meeting physical activity guidelines was associated with the MHO phenotype independent of fitness is, however, novel. If confirmed, our findings indicate that public health messages that encourage active lifestyles to promote fitness should be encouraged regardless of weight status.